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Season 1 opens with the main character (nicknamed "Gary" by the creator) waking up in the middle of a facility. He finds an HEV Suit and a machine gun and heads out into the open. He's immediately attacked by Combine troops, but manages to kill them and venture deeper into Sigma. After killing off most of the Combine the military drops in and disposes of the dwindling soldiers, and turn their sights on Gary. Gary survives long enough for a "cover up" squad who assist Gary in killing off the rest of the soldiers. Gary rests and awakes the next day to find the troops are now gone and have evacuated the remaining scientists. Gary then takes it upon himself to rid the world of Sigma forever. He sends explosives down into the base's core and escapes on a helicopter as Sigma is presumably destroyed in the resulting nuclear explosion.

The next season of HL2 Sigma is actually a prequel to the first season. A scientist enters Xen and returns to find that everyone is dead. Scouts from the military drop in to inspect the incident, and find the scientist is the only survivor. They begin hunting the scientist, who even manages to find an unconscious Gary. Eventually the scientist manages to kill off the soldiers, but not before they are able to send a distress call to the army. Injured and near death, the scientist hobbles towards the exit, the safe haven, his escape. As soon as he opens the door a Combine Gunship shoots him dead, signifying the Combine have found Sigma.

Season 3 shows that Gary is now living in the Combined-controlled Tokyo, City 08. On his way to get a drink at his workplace he finds a secret entrance to a rebel base. Through cracks in the wall he can see two soldiers doing...something. They spot him and open fire, but Gary jumps out of the way. He finds a gun and shoots both soldiers dead, but is unable to prevent them from sending an alert to the City 08 Citadel. Knowing what's coming, Gary dashes back to his apartment only to find the Combine has raided his building and are waiting for him. Gary kills the ambush squad and stocks up on weapons, including the original gun from Season 1. He flees with the Combine in hot pursuit. He escapes City 08 through the sewers and finds himself in the outlands, with the City 08 Citadel and it's fortress of surroundings. Gary finds the Combine have amassed an entire army in preparation for Gary's arrival. Gary single-handedly fights his way into the Citadel, where after killing the guards and freeing the Rebels, begins the self destruct sequence. As the Citadel falls apart Gary finds he cannot get to a safe distance in time. He leads the Rebels to safety and watches as the Citadel appears to vanish in a flash of light and in a ball of fire. We then see what appears to be Gary fall to the ground and remain motionless.

An epilogue reveals Rebel Medics scout the site of the former Citadel. One comes across the motionless body of Gary and the episode suddenly stops, without any further indication of Gary's condition.

Gary, revealed to be alive, wakes suddenly to find he is in a Combine holding facility. He makes his way along the corridors to see his cell guards are dead and they're apparent killers as well: the friendly Soldiers from Season 1 and strange men in blue HEV suits. He follows the carnage to a loading bay where it seems the final battle had taken place. Before he turns to leave he sees a corpse holding a strange weapon, he picks it up and tries to use it. After looting the corpses Gary tries to find the exit, only to find soldiers are waiting for him. He kills them and runs out to find he is in the ruins of City 08. Pieces of the Citadel lay scattered among the wreckage. He enters a gas station to find weapons. As he ventures out he finds soldiers are on his tail. He runs into a camp as the soldiers are killed. Suddenly, men in the same blue suits as the corpses from the facility approach Gary and lead him into an underground tunnel. Gary recuperates and runs out to destroy a gunship. After he heals himself there is a sudden explosion and gunfire as the facility is shaken. He runs up to find a man in a blue suit dead along side a heavily-armored Combine soldier. He runs through the exit just in time to see a soldier interrogating a suited man. As the soldier notices Gary, he quickly executes the man as soldiers advance to the camp. Gary dashes out of the camp and up a hill, where he sees the wreckage of a house and trailer. He goes into the trailer to find it is riddled with corpses, so he goes into the house. He searches it to find no one is there, and runs to a secluded room to hide. As he opens the door, a soldier barges through and kicks Gary. The screen goes white as text spelling, "Do you remember?" appears. The scene then transitions to Gary's lifeless body laying at the hands of the soldier, as more are on their way. More text appears, and we get a constant switch from text to imagery. The text tells Gary his HEV suit has finally ceased function, all the while an unseen figure breaks one of the house's windows and kills the soldier. As the text informs Gary he is finally dying, the unseen figure throws a soldier through a window and rushes into the house as he notices Gary. The text, now seemingly an entity, tells Gary to think of times before. It brings him back to Sigma, and immediately after he destroyed it. He is flying in the helicopter as it suddenly breaks down and crashes into a woodland area, apparently Gary's hometown. As an injured Gary makes his way across the area, he finds allegedly his own house, and as he opens the door the text suddenly obscures the view, saying Gary has "found his parents".

In any Half-Life related series of BedrockPerson's there is no sound. This is due to Bedrock's recording software not being able to record video and audio at the same time. (Though he jokingly says "Gordon Freeman is in charge of SFX")

Since the series' cancellation, there has been little mention of what happened to Gary. Sigma later reappeared in Joe and Jerry Learn the Truth, wherein it's implied that Gary in fact died of radiation poisoning.

BedrockPerson once released a teaser picture for Episode 4 of Sigma REDUX, shown here:

Spoiler showing a heavily-armored Soldier pointing as Soldiers storm what seems to be the camp.